Zinc in PDB 8w9c: Cryo-Em Structure of the RPD3S Complex From Budding Yeast

Other elements in 8w9c:

The structure of Cryo-Em Structure of the RPD3S Complex From Budding Yeast also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the RPD3S Complex From Budding Yeast (pdb code 8w9c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Cryo-Em Structure of the RPD3S Complex From Budding Yeast, PDB code: 8w9c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8w9c

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Zinc binding site 1 out of 7 in the Cryo-Em Structure of the RPD3S Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the RPD3S Complex From Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1000

b:57.3
occ:1.00
 ND1 E:HIS283 2.3 48.1 1.0
SG E:CYS263 2.3 60.6 1.0
SG E:CYS266 2.3 47.1 1.0
NH1 C:ARG300 2.7 27.2 1.0
SG E:CYS286 2.8 40.7 1.0
CG E:HIS283 2.8 48.1 1.0
CB E:HIS283 3.0 48.1 1.0
CE1 E:HIS283 3.2 48.1 1.0
CB E:CYS263 3.3 60.6 1.0
CB E:CYS286 3.5 40.7 1.0
CZ C:ARG300 3.9 27.2 1.0
CD2 E:HIS283 3.9 48.1 1.0
CB E:CYS266 4.0 47.1 1.0
NE2 E:HIS283 4.1 48.1 1.0
N E:HIS283 4.1 48.1 1.0
CA E:HIS283 4.2 48.1 1.0
N E:CYS266 4.3 47.1 1.0
NH2 C:ARG300 4.4 27.2 1.0
CB E:ALA265 4.7 48.8 1.0
CA E:CYS263 4.7 60.6 1.0
CA E:CYS266 4.7 47.1 1.0
NE C:ARG300 4.8 27.2 1.0
CA E:CYS286 4.9 40.7 1.0
N E:CYS286 5.0 40.7 1.0

Zinc binding site 2 out of 7 in 8w9c

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of the RPD3S Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the RPD3S Complex From Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:114.3
occ:1.00
 SG E:CYS303 2.4 82.8 1.0
SG E:CYS275 2.4 85.8 1.0
SG E:CYS306 2.5 84.1 1.0
SG E:CYS278 2.5 87.1 1.0
CB E:CYS306 3.1 84.1 1.0
CB E:CYS275 3.2 85.8 1.0
N E:CYS303 3.2 82.8 1.0
CB E:CYS303 3.4 82.8 1.0
CB E:CYS278 3.6 87.1 1.0
CA E:CYS303 3.9 82.8 1.0
N E:CYS278 3.9 87.1 1.0
C E:HIS302 4.2 86.8 1.0
CA E:HIS302 4.3 86.8 1.0
N E:CYS306 4.3 84.1 1.0
CB E:THR277 4.3 85.6 1.0
CA E:CYS306 4.3 84.1 1.0
CA E:CYS278 4.4 87.1 1.0
CB E:HIS302 4.5 86.8 1.0
C E:CYS303 4.6 82.8 1.0
CA E:CYS275 4.7 85.8 1.0
O E:CYS303 4.8 82.8 1.0
N E:THR277 4.8 85.6 1.0
C E:THR277 4.8 85.6 1.0
CA E:THR277 4.9 85.6 1.0

Zinc binding site 3 out of 7 in 8w9c

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of the RPD3S Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the RPD3S Complex From Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:53.3
occ:1.00
 CB E:CYS466 2.2 40.3 1.0
SG E:CYS443 2.2 29.5 1.0
SG E:CYS440 2.2 28.9 1.0
CB E:CYS440 2.4 28.9 1.0
SG E:CYS466 2.5 40.3 1.0
CA E:CYS466 3.4 40.3 1.0
N E:CYS466 3.5 40.3 1.0
CB E:CYS443 3.8 29.5 1.0
CA E:CYS440 3.9 28.9 1.0
N E:CYS443 4.0 29.5 1.0
NE2 E:HIS469 4.1 26.4 1.0
O E:THR445 4.1 31.7 1.0
N E:THR445 4.2 31.7 1.0
CB E:THR445 4.3 31.7 1.0
CD2 E:HIS469 4.3 26.4 1.0
CA E:CYS443 4.4 29.5 1.0
N E:GLN444 4.4 29.3 1.0
C E:CYS440 4.5 28.9 1.0
OG1 E:THR445 4.6 31.7 1.0
C E:CYS466 4.6 40.3 1.0
C E:CYS443 4.6 29.5 1.0
N E:CYS440 4.6 28.9 1.0
CA E:THR445 4.7 31.7 1.0
C E:LYS465 4.8 34.5 1.0
N E:ASP441 4.9 25.8 1.0
C E:THR445 4.9 31.7 1.0
NE1 E:TRP447 4.9 45.2 1.0
N E:TYR442 5.0 26.6 1.0

Zinc binding site 4 out of 7 in 8w9c

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of the RPD3S Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the RPD3S Complex From Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1003

b:66.0
occ:1.00
 ND1 E:HIS448 2.2 35.5 1.0
SG E:CYS420 2.3 31.1 1.0
SG E:CYS451 2.3 25.9 1.0
CG E:HIS448 3.0 35.5 1.0
CE1 E:HIS448 3.2 35.5 1.0
CB E:HIS448 3.3 35.5 1.0
CB E:CYS420 3.7 31.1 1.0
SG E:CYS417 3.9 34.8 1.0
CB E:CYS451 4.0 25.9 1.0
CD2 E:HIS448 4.2 35.5 1.0
CB E:CYS417 4.2 34.8 1.0
NE2 E:HIS448 4.3 35.5 1.0
CA E:HIS448 4.6 35.5 1.0
N E:CYS451 4.7 25.9 1.0
N E:HIS448 4.8 35.5 1.0
N E:CYS420 4.8 31.1 1.0
CA E:CYS451 4.8 25.9 1.0
CA E:CYS420 4.9 31.1 1.0
CD E:ARG424 5.0 31.6 1.0

Zinc binding site 5 out of 7 in 8w9c

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of the RPD3S Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the RPD3S Complex From Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1000

b:31.0
occ:1.00
 OD2 B:ASP274 2.0 27.3 1.0
OD1 B:ASP186 2.0 27.5 1.0
CG B:ASP186 2.8 27.5 1.0
OD2 B:ASP186 2.9 27.5 1.0
ND1 B:HIS188 2.9 45.2 1.0
CG B:ASP274 3.0 27.3 1.0
CB B:HIS188 3.4 45.2 1.0
OD1 B:ASP274 3.4 27.3 1.0
CG B:HIS188 3.6 45.2 1.0
N B:HIS188 4.0 45.2 1.0
CE1 B:HIS188 4.1 45.2 1.0
CB B:ASP186 4.1 27.5 1.0
OH B:TYR313 4.3 34.2 1.0
NE2 B:HIS150 4.3 27.0 1.0
CB B:ASP274 4.3 27.3 1.0
NE2 B:HIS151 4.3 26.1 1.0
CA B:HIS188 4.3 45.2 1.0
CA B:GLY311 4.4 25.8 1.0
CG1 B:VAL187 4.5 34.6 1.0
CE1 B:HIS150 4.6 27.0 1.0
N B:GLY311 4.6 25.8 1.0
N B:VAL187 4.7 34.6 1.0
CD2 B:HIS188 4.9 45.2 1.0
CE2 B:TYR313 4.9 34.2 1.0

Zinc binding site 6 out of 7 in 8w9c

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of the RPD3S Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the RPD3S Complex From Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1000

b:113.3
occ:1.00
 ND1 F:HIS283 2.2 92.9 1.0
SG F:CYS286 2.5 88.6 1.0
CB F:CYS263 2.7 95.4 1.0
CE1 F:HIS283 2.8 92.9 1.0
CB F:CYS266 3.1 94.3 1.0
CG F:HIS283 3.4 92.9 1.0
N F:CYS266 3.4 94.3 1.0
NH1 D:ARG303 3.6 91.5 1.0
SG F:CYS263 3.7 95.4 1.0
O F:CYS263 3.7 95.4 1.0
CA F:CYS266 3.9 94.3 1.0
NE2 F:HIS283 4.0 92.9 1.0
CA F:CYS263 4.0 95.4 1.0
CB F:CYS286 4.1 88.6 1.0
CB F:HIS283 4.1 92.9 1.0
C F:CYS263 4.1 95.4 1.0
CB F:ALA265 4.2 90.5 1.0
C F:ALA265 4.3 90.5 1.0
CD2 F:HIS283 4.3 92.9 1.0
N F:HIS283 4.4 92.9 1.0
CZ D:ARG303 4.6 91.5 1.0
CA F:ALA265 4.6 90.5 1.0
NH2 D:ARG303 4.6 91.5 1.0
SG F:CYS266 4.6 94.3 1.0
N F:ALA265 4.6 90.5 1.0
C F:CYS266 4.6 94.3 1.0
NH1 D:ARG300 4.7 91.0 1.0
N F:CYS263 4.8 95.4 1.0
N F:ASN267 4.8 94.2 1.0
O F:GLN268 4.8 95.2 1.0
CA F:HIS283 4.9 92.9 1.0

Zinc binding site 7 out of 7 in 8w9c

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Zinc binding site 7 out of 7 in the Cryo-Em Structure of the RPD3S Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of the RPD3S Complex From Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:114.7
occ:1.00
 SG F:CYS306 2.5 89.6 1.0
CB F:CYS278 2.5 93.1 1.0
SG F:CYS275 2.8 96.3 1.0
N F:CYS303 3.0 96.3 1.0
CB F:CYS275 3.3 96.3 1.0
CB F:CYS306 3.3 89.6 1.0
CB F:CYS303 3.4 96.3 1.0
SG F:CYS303 3.5 96.3 1.0
CA F:CYS303 3.6 96.3 1.0
N F:CYS278 3.6 93.1 1.0
CA F:CYS278 3.7 93.1 1.0
SG F:CYS278 3.7 93.1 1.0
N F:CYS306 3.8 89.6 1.0
OE2 F:GLU305 3.9 91.5 1.0
C F:HIS302 3.9 97.9 1.0
CB F:HIS302 4.0 97.9 1.0
O F:CYS303 4.0 96.3 1.0
CA F:HIS302 4.0 97.9 1.0
C F:CYS303 4.1 96.3 1.0
CA F:CYS306 4.2 89.6 1.0
C F:THR277 4.6 91.4 1.0
CD2 F:HIS302 4.7 97.9 1.0
CG F:HIS302 4.8 97.9 1.0
CA F:CYS275 4.8 96.3 1.0
C F:CYS278 4.8 93.1 1.0
C F:GLU305 5.0 91.5 1.0
N F:GLU305 5.0 91.5 1.0
CD F:GLU305 5.0 91.5 1.0
CB F:GLU305 5.0 91.5 1.0

Reference:

C.Wang, C.Chu, Z.Guo, X.Zhan. Structures and Dynamics of RPD3S Complex Bound to Nucleosome. Sci Adv V. 10 K7678 2024.
ISSN: ESSN 2375-2548
PubMed: 38598631
DOI: 10.1126/SCIADV.ADK7678
Page generated: Thu Oct 31 13:14:15 2024

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